Objective To evaluate the psychological status of primary healthcare workers in Shanghai during the novel coronavirus epidemic in the past three years, analyze the related factors, and provide a scientific basis for follow-up intervention and management. Methods A questionnaire survey was conducted from January to February in 2023 among the healthcare workers in Shanghai primary care institutions, their basic personal information and survey results were collected to clarify the mental health status during the epidemic, and the related factors were analyzed. Results There were 72.0% and 57.6% of Shanghai primary health care workers suffered depression and anxiety, respectively. Work-family conflict was positively associated with depression(r=0.391, P<0.05) and anxiety(r=0.370, P<0.05). The total work-family conflict scores were higher among nurses and the healthcare workers who had associate or lower degree, had higher job stress, work intensity or lower salary satisfaction, 11%-30% decreased annual income than that before the epidemic, or participated in public health emergency management previously (P<0.05); depression and anxiety scale scores were higher among nurse and healthcare workers who were female, 30-39 years old, had associate or lower degree, intermediate title, <10 years of work experience, and had higher job stress and work intensity, or less salary satisfaction, or participated in epidemic-related public health emergency management previously. Conclusions The novel coronavirus epidemic showed negative impact on the mental health of primary healthcare workers in Shanghai. Increasing salary and wages, conducting psychological counseling and guidance, and rationalizing work shift, rotation and scheduling can improve the psychological health in primary healthcare staff.